The evolutionary histories of two genetic loci in Drosophila species are being examined by studying genetic variation at the DNA level in natural populations. A methodology has been developed to identify classes of haplotypes in large samples (100 lines or greater). The method involves probing filters containing an image of genomic DNA cut with four-cutter restriction enzymes and run under denaturing conditions on DNA sequencing-type gels. Approximately 20% of all nucleotide polymorphisms and all length polymorphisms can be identified within the probed region. This approach is being applied to samples of approximately 100 lines from each of several populations of D. melanogaster and a single population of its sibling species, D. simulans. Two loci are under investigation - Alcohol dehydrogenase and White.